gene regulation in cancer
DESCRIPTION
Gene regulation in cancer. 11/14/07. Overview. The hallmark of cancer is uncontrolled cell proliferation. Oncogenes code for proteins that help to regulate cell growth and differentiation. A mutation in an oncogene causes uncontrolled cell growth. - PowerPoint PPT PresentationTRANSCRIPT
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Gene regulation in cancer
11/14/07
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Overview
• The hallmark of cancer is uncontrolled cell proliferation.
• Oncogenes code for proteins that help to regulate cell growth and differentiation. A mutation in an oncogene causes uncontrolled cell growth.
• Tumor suppressors suppress cell division or promote apoptosis (regulated cell-death).
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Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Signal• Steroid receptor
TF
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Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
SignalTF
• Steroid receptor
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Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Signal
*TF
• Steroid receptor
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Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Kinase
Signal
TF
• Steroid receptor• Nuclear TF
![Page 7: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/7.jpg)
Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Kinase
TF
Signal• Steroid receptor• Nuclear TF
![Page 8: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/8.jpg)
Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Signal
Kinase
*
TF
• Steroid receptor• Nuclear TF
![Page 9: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/9.jpg)
Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Signal
Kinase
*TF
• Steroid receptor• Nuclear TF
![Page 10: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/10.jpg)
Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Signal
Kinase
*TF
• Steroid receptor• Nuclear TF
![Page 11: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/11.jpg)
Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
TF
Signal• Steroid receptor• Nuclear TF• Latent cytoplasmic TF
![Page 12: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/12.jpg)
Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
TF
Signal• Steroid receptor• Nuclear TF• Latent cytoplasmic TF
![Page 13: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/13.jpg)
Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Signal
TF
*
• Steroid receptor• Nuclear TF• Latent cytoplasmic TF
![Page 14: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/14.jpg)
Different paths leading to transcription factor activation
extra-cellular
cytoplasm
nucleus
Signal
TF
*
• Steroid receptor• Nuclear TF• Latent cytoplasmic TF
![Page 15: Gene regulation in cancer](https://reader035.vdocuments.mx/reader035/viewer/2022062519/56814ff2550346895dbdbca9/html5/thumbnails/15.jpg)
Transcription factors in cancer
Oncogenes• Steroid receptors
– Estrogen receptors (breast cancer) and androgen receptors (prostate cancer)
• Nuclear proteins– JUN
• Latent cytoplasmic factors– STAT
Tumor suppressors• p53, RB, etc.
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Example: STAT pathway
Darnell 2000
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P53: overview
• Known as the “guardian of the genome”
• The first discovered tumor suppressor
• Inactivated in most types of tumors.
• 10,000 tumor related mutations have been identified from human to clam.
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P53: overview
• Sequence-specific transcription factor (both an activator and a repressor)
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Vousden and Lane 2007
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(Vogelstein et al. 2000)
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p53 pathway
Oren 2003
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Oren 2003
Different biological outcomes
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p53 activation
• Nuclear protein
• Activated by phosphorylation.
• Contain multiple phosphorylation sites.
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Different activation of different subsets of genes.
Oren 2003
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Life and death choices of p53
• How do p53 choose which set of genes to activate?
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Life and death choices of p53
• How do p53 choose which set of genes to activate?– Different modifications– Different partners– Others?
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What genes are regulated by p53?
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Gene expression profiling
• Ovarian cancer cell line (p53 is inactivated)• Expression p53 by infection with adenovirus• Label the DNA from the two cell lines differently
and hybridize using a 2-color microarray• Measure gene expression by microarray (60,000
cDNAs) at multiple time points.• Monitor whether genes are activated or
repressed (fold change > 2.5).
Mirza et al. 2003
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Mirza et al. 2003
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Mirza et al. 2003
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Target genes
• Differentially expressed genes can be due to direct or indirect regulation. How to identify direct targets?
Mirza et al. 2003
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Target genes
• Differentially expressed genes can be due to direct or indirect regulation. How to identify direct targets?
• Use known motif information, scan genome for motif sites. These sites are viewed as target genes.
• 294 repressed genes contain p53 motif sites; 67 activated genes contain p53 motif sites
Mirza et al. 2003
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Identifying p53 targets by CHIP-chip
Cawley et al. 2004
• Affymetrix tiling array chr 21 and 22
• 35 bp resolution on average
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Identifying p53 targets by CHIP-chip
Cawley et al. 2004
Data analysis
• Apply Wilcoxon rank-sum test to probes in each sliding window
• P-value cutoff at 10-5
• 1600 p53 sites identified.
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Cawley et al. 2004
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Distribution of TFBS
Cawley et al. 2004
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Novel transcript related to TFBS
Cawley et al. 2004
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Novel transcript related to TFBS
Cawley et al. 2004
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Co-expression between coding and non-coding RNA
Cawley et al. 2004
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Can tiling array data be used to obtain a better motif?
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CHIP-PET: A new method for detecting TFBS
(Wei et al. 2006)
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(Wei et al. 2006)
coun
ts
Detected 122 novel target genes.7
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Motif finding from CHIP-PET data
(Wei et al. 2006)
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Expression profile from multiple tumors
• 193 tumors with p53 wild-type
• 58 tumors with p53 mutant
• Measure gene expression for each tumor tissue
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Expression profile from multiple tumors
• 193 tumors with p53 wild-type
• 58 tumors with p53 mutant
• Measure gene expression for each tumor tissue
Idea:
• For p53 target genes, differential expression should be observed.
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Gene expression profile of p53 wild-type vs mutant tumors
(Wei et al. 2006)
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Gene expression profile of p53 wild-type vs mutant tumors
(Wei et al. 2006)
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Clinical implications
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p53 network
(Vogelstein et al. 2000)
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Oren 2003
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Reading List
• Oren 2003– A review of p53 pathway
• Mirza et al. 2003– Gene expression profile of p53
• Cawley et al. 2004– Map p53 binding sites using high resolution tiling
array• Wei et al. 2006
– Use CHIP-PET to map p53 binding sites, rediscovered p53 motif; linked p53 targets with gene expression profile